forgive me for tooting my own horn, but I believe that this is how its done:
http://www.bay12games.com/cgi-local/ultimatebb.cgi?ubb=get_topic&f=11&t=000714 http://mkv25.net/dfma/map-875-morulingtak
edit: to answer the question you actually ASKED though, i've not had that problem. the only problem ive ever had with cage traps, is the animals over running them before they could be reloaded. the animals will generally continue moving a few squares past the caged leader, and this is usually sufficient to cage the other animals.
unless you run out of cages, of course. the 2-wide solution does sound ideal. you might consider supplimenting your inner door with some raiseable bridges in case of a seige. nothing like having trolls knock down the door to your animal trap.
you dont actually have to worry about wither animals can take an alternate path, as if you want to shut off the trap you can just leave the animals isolated on whatever part of the map they happen to be on, until they make a different pathfinding decision. you DO need an alternate path for your dwarfs, however. so its a good thing you have the smaller inner passage.
unfortuneatly you cant set a door to allow animals but forbid dwarfs. it would make things like this much easier. i guess we can do that in the new version though, by simply forbidding the passageway instead of the door.
[ September 26, 2007: Message edited by: puke ]